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Couple of updates in R-packages

Couple of updates in R-packages

During the last weeks I updated a couple of my R-packages. The main work went into the GenomicTools package, though it required also adjustments to the two packages GenomicTools.fileHandler and hoardeR.

The changes are mainly in user-friendliness and bugfixing to catch special cases of data inputs. If someone uses the packages and finds any other bugs or has suggestions for improvements, please drop me an email, or contact me via the corresponding GitHub project page of the packages.

Manuscript conditionally accepted for publication

Manuscript conditionally accepted for publication

Our Manuscript ‘Computing the Oja Median in R: The Package OjaNP’ with Karl Mosler, Jyrki Möttönen, Klaus Nordhausen, Oleksii Pokotylo and Daniel Vogel got conditionally accepted for publication in the ‘Journal of Statistical Software’. However, the publication will unfortunately take still a while, the Editor wrote to me that ‘Due to various major changes in JSS over the last years, the publication delay (between being added to the queue and final publication) is currently about one year.‘.

In that sense, you can still check out an earlier, unformatted version here from ArXiv or contact me for the latest version of it. I’ll be happy to share the final version of the document with you.

New publication

New publication

Our publication “Validated quantitative trait loci for eggshell quality in experimental and commercial laying hens” has been published as short communication in Animal Genetics.


Compromised eggshell quality causes considerable economic losses for the egg industry. Breeding for improved eggshell quality has been very challenging. Eggshell quality is a trait that would greatly benefit from marker‐assisted selection, which would allow the selection of sires for their direct contribution to the trait and would also allow implementation of measurements integrating a number of shell parameters that are difficult to measure. In this study, we selected the most promising autosomal quantitative trait loci (QTL) affecting eggshell quality on chromosomes 2, 3, 6 and 14 from earlier experiments and we extended the F2 population to include 1599 F2 females. The study was repeated on two commercial populations: Lohmann Tierzucht Rhode Island Red line (n = 692 females) and a Hy‐Line White Plymouth Rock line (n = 290 progeny tested males). We analyzed the selected autosomal QTL regions on the three populations with SNP markers at 4–13 SNPs/Mb density. QTL for eggshell quality were replicated on all studied regions in the F2 population. New QTL were detected for eggshell color on chromosomes 3 and 6. Marker associations with eggshell quality traits were validated in the tested commercial lines on chromosomes 2, 3 and 6, thus paving the way for marker‐assisted selection for improved eggshell quality.

New publication

New publication

The November issue of Computer Methods and Programs in Biomedicine
contains an article about my R-package ‘GenomicTools’:

Screenshot of

The R-package GenomicTools for multifactor dimensionality reduction and the analysis of (exploratory) Quantitative Trait Loci

Background and objectives

We introduce the R-package GenomicTools to perform, among others, a Multifactor Dimensionality Reduction (MDR) for the identification of SNP-SNP interactions. The package further provides a new class of tests for an (exploratory) Quantitative Trait Loci analysis that overcomes some of the limitations of other popular (e)QTL approaches. Popular (e)QTL approaches that use linear models or ANOVA are often based on over-simplified models that have weak statistical properties and which are not robust against outlying observations.


The algorithm to calculate the MDR is well established. To speed up its calculation in R, we implemented it in C++. Further, our implementation also supports the combination of several MDR results to an MDR ensemble classifier. The (e)QTL test procedure is based on a generalized Mann-Whitney test that is tailored for directional alternatives, as they are present in an (e)QTL analysis.


Our package GenomicTools provides functions to determine SNP combinations that have the highest accuracy for a MDR classification problem. It also provides functions to combine the best MDR results to a joined ensemble classifier for improved classification results. Further, the (e)QTL analysis is based on a solid statistical theory. In addition, informative visualizations of the results are provided.


The here presented new class of tests and methods have an easy to apply syntax, so that also researchers inexperienced in R are able to apply our proposed methods and implementations. The package creates publication ready Figures and hence could be a valuable tool for genomic data analysis.